Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 105 of 198
Found at i:33662762 original size:16 final size:17
Alignment explanation
Indices: 33662697--33662840 Score: 62
Period size: 17 Copynumber: 7.7 Consensus size: 17
33662687 TTAAATGTTA
33662697 TGTGATTATATGAGTAT
1 TGTGATTATATGAGTAT
33662714 TGTGA-TATAGCTTGAATGT-T
1 TGTGATTATA---TG-A-GTAT
33662734 ATGTGATTATATGAGTAT
1 -TGTGATTATATGAGTAT
*
33662752 TGTGATATATGCTTGAATGT-T
1 TGTGAT-TAT--ATG-A-GTAT
33662773 ATGTGATTATATGAGTAT
1 -TGTGATTATATGAGTAT
* * *
33662791 AGTGATATATGCTTGAGCATT
1 TGTGAT-TAT--ATGAGTA-T
33662812 ATGTGATTATATGAGTAT
1 -TGTGATTATATGAGTAT
*
33662830 TATGA-TATATG
1 TGTGATTATATG
33662841 CTTAAATGTT
Statistics
Matches: 98, Mismatches: 9, Indels: 41
0.66 0.06 0.28
Matches are distributed among these distances:
16 10 0.10
17 24 0.24
18 11 0.11
19 11 0.11
20 9 0.09
21 16 0.16
22 17 0.17
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.44
Consensus pattern (17 bp):
TGTGATTATATGAGTAT
Found at i:33662777 original size:39 final size:39
Alignment explanation
Indices: 33662668--33662882 Score: 333
Period size: 39 Copynumber: 5.5 Consensus size: 39
33662658 AACATGTTTT
* *
33662668 TGAGTATTGTGGTATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
33662707 TGAGTATTGTGATATA-GCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
33662745 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* ***
33662784 TGAGTATAGTGATATATGCTTGAGCATTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* *
33662823 TGAGTATTATGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* *
33662862 TGTGTAATGTGATATATGCTT
1 TGAGTATTGTGATATATGCTT
33662883 AAAAGTGAAT
Statistics
Matches: 160, Mismatches: 15, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
38 37 0.23
39 123 0.77
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
Found at i:33672777 original size:15 final size:16
Alignment explanation
Indices: 33672757--33672791 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
33672747 AGATAAATAC
*
33672757 AAATACTTAA-AAAAT
1 AAATACTTAAGAAAAG
33672772 AAATACTTAAGAAAAG
1 AAATACTTAAGAAAAG
33672788 AAAT
1 AAAT
33672792 TTCCCCCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (16 bp):
AAATACTTAAGAAAAG
Found at i:33673038 original size:19 final size:18
Alignment explanation
Indices: 33673009--33673057 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
33672999 ATTGAACATA
33673009 AAAATAAAAAT-AAAATTG
1 AAAATAAAAATGAAAA-TG
*
33673027 GAAATAAAAAATGAAAATG
1 AAAAT-AAAAATGAAAATG
33673046 AAAATGAAAAAT
1 AAAAT-AAAAAT
33673058 TTCTTTTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.18
Consensus pattern (18 bp):
AAAATAAAAATGAAAATG
Found at i:33676377 original size:11 final size:11
Alignment explanation
Indices: 33676361--33676386 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
33676351 ATTATAAATT
33676361 AAATAAAAACC
1 AAATAAAAACC
33676372 AAATAAAAACC
1 AAATAAAAACC
33676383 AAAT
1 AAAT
33676387 TACAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.12
Consensus pattern (11 bp):
AAATAAAAACC
Found at i:33682949 original size:22 final size:22
Alignment explanation
Indices: 33682923--33682966 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
33682913 AAAAACCCAA
33682923 AAACA-AAGAACTCTCAAAATGT
1 AAACACAA-AACTCTCAAAATGT
* *
33682945 AAACACAAAATTCTCTAAATGT
1 AAACACAAAACTCTCAAAATGT
33682967 GTTATGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.52, C:0.18, G:0.07, T:0.23
Consensus pattern (22 bp):
AAACACAAAACTCTCAAAATGT
Found at i:33683431 original size:41 final size:41
Alignment explanation
Indices: 33683353--33683441 Score: 106
Period size: 41 Copynumber: 2.2 Consensus size: 41
33683343 GCCTACACGA
** * *
33683353 CCGTGTGAAGGAGGGACATGCCGTGTCACAGATGCACACAT
1 CCGTGTGAAGGAGGGACACACCCTGTCACAGAGGCACACAT
* * * *
33683394 TCGTGTGAAGGAGGGACACACCCTGTGATAGAGGCACACGT
1 CCGTGTGAAGGAGGGACACACCCTGTCACAGAGGCACACAT
33683435 CCGTGTG
1 CCGTGTG
33683442 GCTAAGACAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.25, C:0.24, G:0.34, T:0.18
Consensus pattern (41 bp):
CCGTGTGAAGGAGGGACACACCCTGTCACAGAGGCACACAT
Found at i:33685515 original size:19 final size:18
Alignment explanation
Indices: 33685493--33685535 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
33685483 ACCCGACCTA
33685493 AAAGTTACGATTGGACC-CC
1 AAAGTTAC-ATTGG-CCACC
33685512 AAAGGTTACATTGGCCACC
1 AAA-GTTACATTGGCCACC
33685531 AAAGT
1 AAAGT
33685536 GACCTGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.18
19 13 0.59
20 5 0.23
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (18 bp):
AAAGTTACATTGGCCACC
Found at i:33686145 original size:21 final size:21
Alignment explanation
Indices: 33686129--33686199 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
33686119 CGACACGCAT
33686129 GTGTGAAAGAGGCACACGACC
1 GTGTGAAAGAGGCACACGACC
33686150 GTGTGAAAGAGGCACACGACC
1 GTGTGAAAGAGGCACACGACC
* ** *
33686171 ATGTGATTGAAGCACAC-ATCC
1 GTGTGAAAGAGGCACACGA-CC
33686192 GTGTGAAA
1 GTGTGAAA
33686200 AATGTCATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.34, C:0.21, G:0.30, T:0.15
Consensus pattern (21 bp):
GTGTGAAAGAGGCACACGACC
Found at i:33698916 original size:15 final size:15
Alignment explanation
Indices: 33698896--33698924 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33698886 CGAAAAATAA
33698896 AGAGAATTTATTCTT
1 AGAGAATTTATTCTT
33698911 AGAGAATTTATTCT
1 AGAGAATTTATTCT
33698925 ATCGAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (15 bp):
AGAGAATTTATTCTT
Found at i:33698964 original size:104 final size:104
Alignment explanation
Indices: 33698829--33699017 Score: 360
Period size: 104 Copynumber: 1.8 Consensus size: 104
33698819 TTCTCTTCTT
*
33698829 ATAAATAGATGGCATCGGAAGGGCATAAAACACAACTTTGAGAGATTGTTACTCTGTCGAAAAAT
1 ATAAATAGATGGCATCGGAAGGGCATAAAACACAACTTTGAGAGATTGTTACTCTGTCAAAAAAT
33698894 AAAGAGAATTTATTCTTAGAGAATTTATTCTATCGAAAA
66 AAAGAGAATTTATTCTTAGAGAATTTATTCTATCGAAAA
*
33698933 ATAAATAGATGGCATTGGAAGGGCATAAAACACAACTTTGAGAGATTGTTACTCTGTCAAAAAAT
1 ATAAATAGATGGCATCGGAAGGGCATAAAACACAACTTTGAGAGATTGTTACTCTGTCAAAAAAT
33698998 AAAGAGAATTTATTCTTAGA
66 AAAGAGAATTTATTCTTAGA
33699018 TATTAAATAT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 83 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.29
Consensus pattern (104 bp):
ATAAATAGATGGCATCGGAAGGGCATAAAACACAACTTTGAGAGATTGTTACTCTGTCAAAAAAT
AAAGAGAATTTATTCTTAGAGAATTTATTCTATCGAAAA
Found at i:33707272 original size:45 final size:46
Alignment explanation
Indices: 33707186--33707273 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 46
33707176 TAAATGAATA
* * *
33707186 GAAATAGAGAAATGGAAAACATTTAGAAATTATTATGGTTTTCTCT
1 GAAATAGAGAAATGGAAAACATTTAGAAATGAATATAGTTTTCTCT
* * * *
33707232 GAAATGGAGAAATGG-AATCATTTGGAAATGAATGTAGTTTTC
1 GAAATAGAGAAATGGAAAACATTTAGAAATGAATATAGTTTTC
33707274 CCAAAATGGA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
45 21 0.60
46 14 0.40
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.33
Consensus pattern (46 bp):
GAAATAGAGAAATGGAAAACATTTAGAAATGAATATAGTTTTCTCT
Found at i:33707288 original size:6 final size:6
Alignment explanation
Indices: 33707277--33707318 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
33707267 AGTTTTCCCA
*
33707277 AAATGG AAATGG AAATGG AAATGG AAATGA AAATGAG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATG-G AAATG
33707319 ATTCGTTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:33717293 original size:16 final size:15
Alignment explanation
Indices: 33717250--33717297 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
33717240 TTTATGACTG
*
33717250 TGTTCATTATT-TTAA
1 TGTT-ATTATTGTTAT
33717265 TGTTATTATTGTTAT
1 TGTTATTATTGTTAT
33717280 TGTTATTCATTGTTAT
1 TGTTATT-ATTGTTAT
33717296 TG
1 TG
33717298 GTTTTATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 6 0.20
15 14 0.47
16 10 0.33
ACGTcount: A:0.21, C:0.04, G:0.12, T:0.62
Consensus pattern (15 bp):
TGTTATTATTGTTAT
Found at i:33717696 original size:2 final size:2
Alignment explanation
Indices: 33717691--33717729 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
33717681 TATATATATA
33717691 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
33717730 TTATATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:33721850 original size:7 final size:7
Alignment explanation
Indices: 33721840--33721902 Score: 58
Period size: 7 Copynumber: 8.9 Consensus size: 7
33721830 AAAAAAAAGG
33721840 AAAAAAC
1 AAAAAAC
33721847 AAAAAA-
1 AAAAAAC
33721853 AACAAAAC
1 AA-AAAAC
*
33721861 AAAAAAA
1 AAAAAAC
33721868 ATAAAAATC
1 A-AAAAA-C
33721877 -AAAAAC
1 AAAAAAC
*
33721883 AAAAATC
1 AAAAAAC
*
33721890 AAAAATC
1 AAAAAAC
33721897 AAAAAA
1 AAAAAA
33721903 ATCGAAGTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
6 3 0.06
7 37 0.79
8 7 0.15
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.06
Consensus pattern (7 bp):
AAAAAAC
Found at i:33721880 original size:13 final size:13
Alignment explanation
Indices: 33721864--33721901 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
33721854 ACAAAACAAA
33721864 AAAAATAAAAATC
1 AAAAATAAAAATC
*
33721877 AAAAACAAAAATC
1 AAAAATAAAAATC
33721890 AAAAATCAAAAA
1 AAAAAT-AAAAA
33721902 AATCGAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (13 bp):
AAAAATAAAAATC
Found at i:33721887 original size:14 final size:14
Alignment explanation
Indices: 33721840--33721902 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 14
33721830 AAAAAAAAGG
33721840 AAAAAA-CAAAAA-
1 AAAAAATCAAAAAC
* *
33721852 AAACAAAACAAAAAAA
1 AAA-AAATC-AAAAAC
33721868 ATAAAAATCAAAAAC
1 A-AAAAATCAAAAAC
33721883 -AAAAATCAAAAATC
1 AAAAAATCAAAAA-C
33721897 AAAAAA
1 AAAAAA
33721903 ATCGAAGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
12 3 0.07
13 15 0.36
14 2 0.05
15 15 0.36
16 5 0.12
17 2 0.05
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.06
Consensus pattern (14 bp):
AAAAAATCAAAAAC
Found at i:33721895 original size:20 final size:19
Alignment explanation
Indices: 33721864--33721901 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
33721854 ACAAAACAAA
33721864 AAAAATAAAAATCAAAAAC
1 AAAAATAAAAATCAAAAAC
33721883 AAAAATCAAAAATCAAAAA
1 AAAAAT-AAAAATCAAAAA
33721902 AATCGAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (19 bp):
AAAAATAAAAATCAAAAAC
Found at i:33721926 original size:26 final size:27
Alignment explanation
Indices: 33721897--33721953 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
33721887 ATCAAAAATC
** * *
33721897 AAAAAAATCGAAGTAAAAA-AAAAGGA
1 AAAAAAAGAGAAGAAAAAAGAAAAAGA
33721923 AAAAAAAGAGAAGAAAAAAGAAAAAGA
1 AAAAAAAGAGAAGAAAAAAGAAAAAGA
33721950 AAAA
1 AAAA
33721954 GGAGAGGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (27 bp):
AAAAAAAGAGAAGAAAAAAGAAAAAGA
Found at i:33721927 original size:13 final size:12
Alignment explanation
Indices: 33721911--33721953 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
33721901 AAATCGAAGT
*
33721911 AAAAAAAAAGGA
1 AAAAAAAAAAGA
33721923 AAAAAAAGAGAAGA
1 AAAAAAA-A-AAGA
33721937 AAAAAGAAAAAGA
1 AAAAA-AAAAAGA
33721950 AAAA
1 AAAA
33721954 GGAGAGGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.26
13 9 0.33
14 9 0.33
15 2 0.07
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:33724204 original size:88 final size:88
Alignment explanation
Indices: 33724055--33724844 Score: 1323
Period size: 88 Copynumber: 9.0 Consensus size: 88
33724045 CAACGAAGTT
* *
33724055 AAAGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCGAAGACATAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
*
33724120 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
*
33724143 AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
33724208 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
* *
33724231 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGTAGGTCGAAGACATAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
* *
33724296 GGTGATGGAGCTGGTTGAAAACA
66 TGTGATGGAGCTGGTTGAAGACA
* *
33724319 AAAGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
* *
33724384 TTTGATGGAGTTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
* *
33724407 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGTAGGTTGAAGACACAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
* *
33724472 GGTGATGGAGCTGGTTGAAAACA
66 TGTGATGGAGCTGGTTGAAGACA
* *
33724495 AAAGATCTTACATTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
*
33724560 TGTGATGAAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
* *
33724583 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCTCTCTCGTT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
33724648 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
* *
33724671 AAAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGAT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
33724736 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
* *
33724759 AAAGATCTTGCCTTCCTGCATTGACAGCGAGGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
33724824 TGTCG-TGGAG-TAGGTTGAAGA
66 TGT-GATGGAGCT-GGTTGAAGA
33724845 TTGCAAATTC
Statistics
Matches: 656, Mismatches: 44, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
87 1 0.00
88 654 1.00
89 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (88 bp):
AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
TGTGATGGAGCTGGTTGAAGACA
Found at i:33724813 original size:44 final size:44
Alignment explanation
Indices: 33724061--33724815 Score: 351
Period size: 44 Copynumber: 17.2 Consensus size: 44
33724051 AGTTAAAGAT
* *
33724061 CTTGCATTCCTGCATTGACAGCGAAGCAGGTCGAAGACATAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
** * * * * *
33724105 CTTGCC-TCTCTCGGTTGTGATA--G-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACACAA-AC
*
33724149 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
** * * * * *
33724193 CTTGCC-TCTCTCGGTTGTGA-TG-G-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACACAA-AC
* *
33724237 CTTGCCTTCCTGCATTGACAGCGAAGTAGGTCGAAGACATAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
* *** * * * * * *
33724281 CTTGCCTCTCTCGGTGGTGA-TG-G-AGCTGGTTGAAAACAAAAGAT
1 CTTGCCT-TC-CTGCATTGACAGCGAAGCAGGTCGAAGACACAA-AC
* *
33724325 CTTGCATTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
* ** * ** * * *
33724369 CTTGCCTCTCTCGGTTTTGA-TG-G-AGTTGGTTGAAGACAAAAGAT
1 CTTGCCT-TC-CTGCATTGACAGCGAAGCAGGTCGAAGACACAA-AC
* *
33724413 CTTGCCTTCCTGCATTGACAGCGAAGTAGGTTGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
* *** * * * * * *
33724457 CTTGCCTCTCTCGGTGGTGA-TG-G-AGCTGGTTGAAAACAAAAGAT
1 CTTGCCT-TC-CTGCATTGACAGCGAAGCAGGTCGAAGACACAA-AC
* *
33724501 CTTACATTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
* ** * * * * *
33724545 CTTGCC-TCTCT-CGGTTGTGA-TGAAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTC-CTGC-ATTGACAGCGAAGCAGGTCGAAGACACAA-AC
*
33724589 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
** * * * * *
33724633 CTTGCC-TCTCTCGTTTGTGA-TG-G-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACACAA-AC
*
33724677 CTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
** * * * *
33724721 CTTGCC-TCTCT-CGATTGTGATG-G-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTC-CTGC-ATTGACA-GCGAAGCAGGTCGAAGACACAA-AC
* *
33724765 CTTGCCTTCCTGCATTGACAGCGAGGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
33724809 CTTGCCT
1 CTTGCCT
33724816 CTCTCGGTTG
Statistics
Matches: 514, Mismatches: 141, Indels: 112
0.67 0.18 0.15
Matches are distributed among these distances:
42 26 0.05
43 146 0.28
44 170 0.33
45 146 0.28
46 26 0.05
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (44 bp):
CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
Found at i:33724987 original size:132 final size:132
Alignment explanation
Indices: 33724828--33725939 Score: 1772
Period size: 132 Copynumber: 8.4 Consensus size: 132
33724818 CTCGGTTGTC
*
33724828 GTGGAGTAGGTTGAAGATTGCAAATTCTGTCACCCTAAGTAGTAGTGGAGCAGATCGAAGATGGT
1 GTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGTAGTAGTGGAGCAGATCGAAGATGGT
*
33724893 GAATCTTATCTTCCCAATACAGTGGAGAAGTAGATTTAAGCCATTAGTCCTATCACCCTAAGCAG
66 GAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAG
33724958 TA
131 TA
*
33724960 GTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAA-TCAGTAGTGGAGCAGATCAAAGATGG
1 GTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGT-AGTAGTGGAGCAGATCGAAGATGG
* * *
33725024 TTAATCTTATCTTCCTAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAACA
65 TGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCA
33725089 GTA
130 GTA
* *
33725092 GTGGAGTAGGTTGAAGATTGCTGATTCTGTCACCCTAA-TCAGTAGTGGAGCAGATCAAAGATGG
1 GTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGT-AGTAGTGGAGCAGATCGAAGATGG
* * *
33725156 TTATTCTTATCTTCCTAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCA
65 TGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCA
33725221 GTA
130 GTA
*
33725224 GTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAA-TCAGTAGTGGAGCAGATCGAAGATGG
1 GTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGT-AGTAGTGGAGCAGATCGAAGATGG
* * *
33725288 TGAATCTTATCTTCCTAATACAGTGGAGAAGCAAATTTAAGCCATTAGTCCTGTCACCCTAAAGC
65 TGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCT-AAGC
33725353 AGTA
129 AGTA
* * *
33725357 GTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAGGCAGTAGTGGAGCAGATCGAAGATGGT
1 GTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGTAGTAGTGGAGCAGATCGAAGATGGT
*
33725422 GAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCTTATCACCCTAAAG-A
66 GAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCT-AAGCA
33725486 GTA
130 GTA
* * * *
33725489 GTGGAGTACGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGAAGCAGATCGAAGATGGT
1 GTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGTAGTAGTGGAGCAGATCGAAGATGGT
33725554 GAATC-TATCTTCCCAATACAGTGGGAGAAGCAGAATTTAAGCCATTAGTCCTATCACCCTAA-C
66 GAATCTTATCTTCCCAATACAGT-GGAGAAGCAG-ATTTAAGCCATTAGTCCTATCACCCTAAGC
33725617 AGTA
129 AGTA
* * * *
33725621 GTAGAGTAGGTTAAAGATTGTAGATTCTGTCACCTTAA-TCAGTAGTGGAGCAGATCGAAGATGG
1 GTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGT-AGTAGTGGAGCAGATCGAAGATGG
* *
33725685 TGAATCTTGTCTTCCCAATATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAA-CA
65 TGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCA
33725749 GTA
130 GTA
* * *
33725752 GTAGAGTAGGTTAAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGT
1 GTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGTAGTAGTGGAGCAGATCGAAGATGGT
* *
33725817 GAATCTTATCTTCCCAATACAGTGGAGAAGCATATTTAAGCCATTAGTCCTATCACCTTAAGCAG
66 GAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAG
33725882 TA
131 TA
* *
33725884 GTGGAGTAGGTTGAAGATTGCAGATTCTGTCCCCCTAAGCAGTAGTGGAGCAGATC
1 GTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGTAGTAGTGGAGCAGATC
33725940 AACAATAACG
Statistics
Matches: 924, Mismatches: 46, Indels: 20
0.93 0.05 0.02
Matches are distributed among these distances:
131 169 0.18
132 586 0.63
133 169 0.18
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (132 bp):
GTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGTAGTAGTGGAGCAGATCGAAGATGGT
GAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAG
TA
Found at i:33724995 original size:44 final size:44
Alignment explanation
Indices: 33724942--33725939 Score: 245
Period size: 44 Copynumber: 22.7 Consensus size: 44
33724932 GCCATTAGTC
* * * *
33724942 CTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGCAGATT
* * * * *
33724986 CTGTCACCCTAATCAGTAGTGGAGCAGATCAAAGATGGTTA-A-T
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTG-CAGATT
** * * * ** *
33725029 CTTATCTTCCTAATACAGTGGAGAAGCAGATTTAAGCCATT--AG-TC
1 C-TATCACCCTAA-ACAGTAGTGGAGCAGATCGAAG--ATTGCAGATT
* * * *
33725074 CTATCACCCTAAACAGTAGTGGAGTAGGTTGAAGATTGCTGATT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGCAGATT
* * * ***
33725118 CTGTCACCCTAATCAGTAGTGGAGCAGATCAAAGA-TGGTTATT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGCAGATT
** * * * ** *
33725161 CTTATCTTCCTAATACAGTGGAGAAGCAGATTTAAGCCATT--AG-TC
1 C-TATCACCCTAA-ACAGTAGTGGAGCAGATCGAAG--ATTGCAGATT
* * *
33725206 CTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGCAGATT
* * ** *
33725250 CTGTCACCCTAATCAGTAGTGGAGCAGATCGAAGA-TGGTGAAT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGCAGATT
** * * * * ** *
33725293 CTTATCTTCCTAATACAGTGGAGAAGCAAATTTAAGCCATT--AG-TC
1 C-TATCACCCTAA-ACAGTAGTGGAGCAGATCGAAG--ATTGCAGATT
* * *
33725338 CTGTCACCCTAAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATT
1 CTATCACCCTAAA-CAGTAGTGGAGCAGATCGAAGATTGCAGATT
* ** ** *
33725383 CTGTCACCCTAGGCAGTAGTGGAGCAGATCGAAGA-TGGTGAAT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGCAGATT
* * * * **
33725426 CTTATCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCATT--AG--T
1 C-TATC-ACCCTAA-ACAGTAGTGGAGCAGATCGAAG--ATTGCAGATT
* *
33725470 CTTATCACCCTAAAGAGTAGTGGAGTACG-TCGAAGATTGCAGATT
1 C-TATCACCCTAAACAGTAGTGGAGCA-GATCGAAGATTGCAGATT
* * * ** *
33725515 CTGTCACCCTAAGCAGTAGTGAAGCAGATCGAAGA-TGGTGAAT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGCAGATT
* * ** *
33725558 CTATCTTCCC-AATACAGT-GGGAGAAGCAGAATTTAAGCCATT--AG-TC
1 CTATC-ACCCTAA-ACAGTAGTG-G-AGCAG-ATCGAAG--ATTGCAGATT
* * * ** *
33725604 CTATCACCCT-AACAGTAGTAGAGTAGGTTAAAGATTGTAGATT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGCAGATT
* * * ** *
33725647 CTGTCACCTTAATCAGTAGTGGAGCAGATCGAAGA-TGGTGAAT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGCAGATT
* * * * * * ** *
33725690 CTTGTCTTCCC-AATATAGTGGAGAAGCAGATTTAAGCCATT--AG-TC
1 C-TATC-ACCCTAA-ACAGTAGTGGAGCAGATCGAAG--ATTGCAGATT
* * * **
33725735 CTATCACCCT-AACAGTAGTAGAGTAGGTTAAAGATTGCAGATT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGCAGATT
* * ** *
33725778 CTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGA-TGGTGAAT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGCAGATT
* * * * * ** *
33725821 CTTATCTTCCC-AATACAGTGGAGAAGCATATTTAAGCCATT--AG-TC
1 C-TATC-ACCCTAA-ACAGTAGTGGAGCAGATCGAAG--ATTGCAGATT
* * * * *
33725866 CTATCACCTTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGCAGATT
* * *
33725910 CTGTCCCCCTAAGCAGTAGTGGAGCAGATC
1 CTATCACCCTAAACAGTAGTGGAGCAGATC
33725940 AACAATAACG
Statistics
Matches: 664, Mismatches: 215, Indels: 150
0.65 0.21 0.15
Matches are distributed among these distances:
40 6 0.01
41 12 0.02
42 26 0.04
43 144 0.22
44 315 0.47
45 132 0.20
46 14 0.02
47 8 0.01
48 6 0.01
49 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (44 bp):
CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGCAGATT
Found at i:33727457 original size:16 final size:15
Alignment explanation
Indices: 33727414--33727461 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
33727404 TTTATGACTG
*
33727414 TGTTCATTATT-TTAA
1 TGTT-ATTATTGTTAT
33727429 TGTTATTATTGTTAT
1 TGTTATTATTGTTAT
33727444 TGTTATTCATTGTTAT
1 TGTTATT-ATTGTTAT
33727460 TG
1 TG
33727462 GTTTTATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 6 0.20
15 14 0.47
16 10 0.33
ACGTcount: A:0.21, C:0.04, G:0.12, T:0.62
Consensus pattern (15 bp):
TGTTATTATTGTTAT
Found at i:33727853 original size:2 final size:2
Alignment explanation
Indices: 33727848--33727872 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33727838 TATATATATA
33727848 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
33727873 TTATATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:33729387 original size:18 final size:19
Alignment explanation
Indices: 33729357--33729401 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
33729347 TATTCTTCAA
33729357 AATTTTATATAAAT-TTTGG
1 AATTTT-TATAAATATTTGG
*
33729376 AATTTTTATAAATATTTTG
1 AATTTTTATAAATATTTGG
33729395 AATTTTT
1 AATTTTT
33729402 TTGTAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (19 bp):
AATTTTTATAAATATTTGG
Found at i:33729402 original size:20 final size:19
Alignment explanation
Indices: 33729357--33729402 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
33729347 TATTCTTCAA
*
33729357 AATTTTATATAAATTTTGG
1 AATTTTTTATAAATTTTGG
*
33729376 AA-TTTTTATAAATATTTTG
1 AATTTTTTATAAAT-TTTGG
33729395 AATTTTTT
1 AATTTTTT
33729403 TGTAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 10 0.43
19 8 0.35
20 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (19 bp):
AATTTTTTATAAATTTTGG
Found at i:33730474 original size:10 final size:9
Alignment explanation
Indices: 33730446--33730472 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
33730436 CGGAAATAAA
33730446 AATATTTTT
1 AATATTTTT
33730455 AATATTTTT
1 AATATTTTT
33730464 AATATTTTT
1 AATATTTTT
33730473 TATGTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
AATATTTTT
Found at i:33733635 original size:8 final size:8
Alignment explanation
Indices: 33733600--33733641 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
33733590 CCAATTCTAA
33733600 TTTTCTTT
1 TTTTCTTT
33733608 TTTCTCTTCT
1 TTT-TCTT-T
*
33733618 TTAT-TTT
1 TTTTCTTT
33733625 TTTTCTTT
1 TTTTCTTT
33733633 TTTTCTTT
1 TTTTCTTT
33733641 T
1 T
33733642 GATTTGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
7 4 0.14
8 17 0.59
9 5 0.17
10 3 0.10
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTCTTT
Found at i:33734528 original size:27 final size:25
Alignment explanation
Indices: 33734472--33734536 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 25
33734462 TTTGTATATG
*
33734472 ATTATTTTAACTTGCTTTATAGATT
1 ATTATTTTAAGTTGCTTTATAGATT
*
33734497 ATTATTTTAAGTTGCTTTATATATT
1 ATTATTTTAAGTTGCTTTATAGATT
33734522 ATTTTATTTTAAGTT
1 A--TTATTTTAAGTT
33734537 ATTCTACATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 24 0.67
27 12 0.33
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.60
Consensus pattern (25 bp):
ATTATTTTAAGTTGCTTTATAGATT
Found at i:33734547 original size:27 final size:26
Alignment explanation
Indices: 33734473--33734559 Score: 79
Period size: 25 Copynumber: 3.3 Consensus size: 26
33734463 TTGTATATGA
* * * *
33734473 TTATTTTAACTTGCTTTATAGATTA-
1 TTATTTTAAGTTGATTTACATATTAC
* * *
33734498 TTATTTTAAGTTGCTTTATATATTATT
1 TTATTTTAAGTTGATTTACATATTA-C
33734525 TTATTTTAAGTT-ATTCTACATATTAC
1 TTATTTTAAGTTGATT-TACATATTAC
33734551 TTATTTTAA
1 TTATTTTAA
33734560 AATTAACCCA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
25 23 0.43
26 11 0.20
27 20 0.37
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.59
Consensus pattern (26 bp):
TTATTTTAAGTTGATTTACATATTAC
Found at i:33747381 original size:44 final size:44
Alignment explanation
Indices: 33746815--33747380 Score: 890
Period size: 44 Copynumber: 13.0 Consensus size: 44
33746805 ATCGAAGATA
* *
33746815 TAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAATATTG
1 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* *
33746859 TAAGTCCTATCTCACTGACCAGCAGTGGAATAGGTGGAAGATTG
1 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
*
33746903 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAAGTGGAAGATTG
1 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
33746947 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
1 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* *
33746991 TAAACCCTATCTCCCT-A--ACCA--GGAATAGGTGGAAGATTG
1 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
**
33747030 TAAGCCCTATCTCCCTGACCAATAGTGGAATAGGTGGAAGATTG
1 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
33747074 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
1 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* *
33747118 TAAGTCCTATCTCCCTAACCAGCAGTGGAATAGGTGGAAGATTG
1 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
*
33747162 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAATATTG
1 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
*
33747206 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAATATTG
1 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
33747250 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
1 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* * * *
33747294 TAAGTCCTATATCCCTGACCAGCAGTGGAATAGGTTGAAGATTA
1 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* * * ** *
33747338 CAAGTCCTATCTCCCTAATTAGCAGTGGAATAGGTGGATGATT
1 TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATT
33747381 AGTTTCTATG
Statistics
Matches: 487, Mismatches: 30, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
39 33 0.07
40 1 0.00
41 3 0.01
42 2 0.00
43 1 0.00
44 447 0.92
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (44 bp):
TAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
Found at i:33749385 original size:17 final size:18
Alignment explanation
Indices: 33749354--33749387 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
33749344 CTAATTTTCC
33749354 TTTTTCTCTTCTTTATTA
1 TTTTTCTCTTCTTTATTA
*
33749372 TTTTTCT-TTTTTTATT
1 TTTTTCTCTTCTTTATT
33749388 TTGATTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTCTCTTCTTTATTA
Found at i:33750277 original size:27 final size:24
Alignment explanation
Indices: 33750222--33750285 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 24
33750212 TTTGTATATG
*
33750222 ATTATTTTAACTTGCTTATACATT
1 ATTATTTTAAGTTGCTTATACATT
*
33750246 ATTATTTTAAGTTGCTTTATATATT
1 ATTATTTTAAGTTGC-TTATACATT
33750271 ATTTTATTTTAAGTT
1 A--TTATTTTAAGTT
33750286 ATTCTACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
24 14 0.40
25 9 0.26
27 12 0.34
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.59
Consensus pattern (24 bp):
ATTATTTTAAGTTGCTTATACATT
Found at i:33750296 original size:27 final size:26
Alignment explanation
Indices: 33750243--33750308 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
33750233 TTGCTTATAC
* *
33750243 ATTA-TTATTTTAAGTTGCTTTATAT
1 ATTACTTATTTTAAGTTGATTTACAT
*
33750268 ATTATTTTATTTTAAGTT-ATTCTACAT
1 ATTA-CTTATTTTAAGTTGATT-TACAT
33750295 ATTACTTATTTTAA
1 ATTACTTATTTTAA
33750309 AATTAACCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 4 0.11
26 11 0.31
27 20 0.57
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.59
Consensus pattern (26 bp):
ATTACTTATTTTAAGTTGATTTACAT
Found at i:33754323 original size:13 final size:14
Alignment explanation
Indices: 33754292--33754324 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
33754282 TTAAAATTAT
*
33754292 ATAAAAGGATATAA
1 ATAAAACGATATAA
33754306 ATAAAACGATAT-A
1 ATAAAACGATATAA
33754319 ATAAAA
1 ATAAAA
33754325 TAAATGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.67, C:0.03, G:0.09, T:0.21
Consensus pattern (14 bp):
ATAAAACGATATAA
Found at i:33756025 original size:21 final size:22
Alignment explanation
Indices: 33755977--33756025 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
33755967 TATGCCCTTG
*
33755977 CATTTCCTCTTTCTTTCTTTCT
1 CATTTTCTCTTTCTTTCTTTCT
*
33755999 CTTTTTCT-TTTCTTTCTGTT-T
1 CATTTTCTCTTTCTTTCT-TTCT
33756020 CATTTT
1 CATTTT
33756026 GGCTTGGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.04, C:0.24, G:0.02, T:0.69
Consensus pattern (22 bp):
CATTTTCTCTTTCTTTCTTTCT
Found at i:33768833 original size:9 final size:9
Alignment explanation
Indices: 33768819--33768850 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
33768809 CCAATATATA
33768819 TTATGTAAG
1 TTATGTAAG
33768828 TTATGTAAG
1 TTATGTAAG
33768837 TTATGTAAG
1 TTATGTAAG
33768846 TTATG
1 TTATG
33768851 ATCCAAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:33769224 original size:19 final size:18
Alignment explanation
Indices: 33769172--33769244 Score: 58
Period size: 19 Copynumber: 3.9 Consensus size: 18
33769162 AATTTCAACA
33769172 TTAA-TAAAAATATTATT
1 TTAATTAAAAATATTATT
** *
33769189 TTCCTTTAAAAAAATTATT
1 TT-AATTAAAAATATTATT
33769208 TTAATTAAATAATATTAATT
1 TTAATTAAA-AATATT-ATT
* * *
33769228 TTTATGATAAATATTAT
1 TTAATTAAAAATATTAT
33769245 ATTATGTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
17 2 0.05
18 7 0.16
19 25 0.58
20 9 0.21
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (18 bp):
TTAATTAAAAATATTATT
Found at i:33771527 original size:18 final size:18
Alignment explanation
Indices: 33771501--33771537 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
33771491 AAATCGATGC
33771501 ATGCCAAAATCAAATCCG
1 ATGCCAAAATCAAATCCG
* *
33771519 ATGCTAAAATTAAATCCG
1 ATGCCAAAATCAAATCCG
33771537 A
1 A
33771538 ACAATAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (18 bp):
ATGCCAAAATCAAATCCG
Found at i:33771981 original size:14 final size:14
Alignment explanation
Indices: 33771964--33771990 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33771954 GTCGAATGAA
33771964 GATTTGGGGAATTT
1 GATTTGGGGAATTT
33771978 GATTTGGGGAATT
1 GATTTGGGGAATT
33771991 AGGGATTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (14 bp):
GATTTGGGGAATTT
Found at i:33772018 original size:14 final size:14
Alignment explanation
Indices: 33771999--33772028 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33771989 TTAGGGATTT
*
33771999 GGGAAAAAAATTAG
1 GGGAAAAAAATAAG
33772013 GGGAAAAAAATAAG
1 GGGAAAAAAATAAG
33772027 GG
1 GG
33772029 ATTTCGAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.33, T:0.10
Consensus pattern (14 bp):
GGGAAAAAAATAAG
Found at i:33772156 original size:40 final size:41
Alignment explanation
Indices: 33772100--33772196 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
33772090 TAAAATTATA
* * *
33772100 CTTTGCGGCGCTTTTTCTCCT-AGCGCCGCTAATGCTTGACC
1 CTTTGCAGCG-TTTTTCTCATAAACGCCGCTAATGCTTGACC
33772141 CTTTGCAGCGTTTTTCTCATAAACGCCGCTAATGCTTGACC
1 CTTTGCAGCGTTTTTCTCATAAACGCCGCTAATGCTTGACC
* *
33772182 TTTTGCAGTGTTTTT
1 CTTTGCAGCGTTTTT
33772197 TCGTTAGTGC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
40 9 0.18
41 41 0.82
ACGTcount: A:0.13, C:0.28, G:0.20, T:0.39
Consensus pattern (41 bp):
CTTTGCAGCGTTTTTCTCATAAACGCCGCTAATGCTTGACC
Found at i:33778220 original size:16 final size:15
Alignment explanation
Indices: 33778172--33778225 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
33778162 AAATAATTAG
* *
33778172 TTAATAATAGTAAAA
1 TTAATAATAATGAAA
* *
33778187 ATAATAATAATTAAA
1 TTAATAATAATGAAA
*
33778202 TTAAATAATAATGATA
1 TT-AATAATAATGAAA
33778218 TTAATAAT
1 TTAATAAT
33778226 TGGGGCATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 19 0.59
16 13 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (15 bp):
TTAATAATAATGAAA
Found at i:33779225 original size:15 final size:14
Alignment explanation
Indices: 33779205--33779234 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
33779195 AGCTACAGGA
33779205 AATAAAAAAAGTTAT
1 AATAAAAAAA-TTAT
33779220 AATAAAAAAATTAT
1 AATAAAAAAATTAT
33779234 A
1 A
33779235 TGGTTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
AATAAAAAAATTAT
Found at i:33782347 original size:19 final size:16
Alignment explanation
Indices: 33782304--33782347 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 16
33782294 GTCGTTCGTT
33782304 TTTAAAATATTATTCA
1 TTTAAAATATTATTCA
33782320 TTTACAAATCATTATTCAA
1 TTTA-AAAT-ATTATTC-A
33782339 TTTCAAAAT
1 TTT-AAAAT
33782348 GTTTTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
18 7 0.29
19 8 0.33
20 1 0.04
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAAATATTATTCA
Found at i:33790685 original size:23 final size:20
Alignment explanation
Indices: 33790659--33790708 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
33790649 GGTTTTTTAG
33790659 TATTTGTGCATATTAGATTTATT
1 TATTTGTGC--ATTA-ATTTATT
*
33790682 TATTCGTGCATTAATTTATT
1 TATTTGTGCATTAATTTATT
*
33790702 TAATTGT
1 TATTTGT
33790709 CTAATGTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.50
21 4 0.17
23 8 0.33
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (20 bp):
TATTTGTGCATTAATTTATT
Found at i:33797988 original size:4 final size:4
Alignment explanation
Indices: 33797973--33798017 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
33797963 CCAATTTTAA
* * * *
33797973 TCAT TTAT TCAT TCAT TCAT CCAT CCAT TCAT TCAT TCAC TCAT T
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT T
33798018 TGTTTACTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (4 bp):
TCAT
Found at i:33801293 original size:42 final size:42
Alignment explanation
Indices: 33801234--33801470 Score: 332
Period size: 42 Copynumber: 5.6 Consensus size: 42
33801224 AAAGAAAGCA
* *
33801234 TTCATTGCATTTAGAGGCCCAGGTGTGGAGG-CCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCC-ATTCACTT
* * *
33801276 TTCATTGTATTTAGAGGCTCAGGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTCACTT
* * *
33801318 TTGATTGCACTTAGAGGCCCAAGTGTGGAGGTCAATTCACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTCACTT
* *
33801360 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTCACTT
* *
33801402 GTCATTGCATTTAGAGGTCCAAGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTCACTT
* *
33801444 TTCATTGCACTTAGAGACCCAAGTGTG
1 TTCATTGCATTTAGAGGCCCAAGTGTG
33801471 TTTCATTGCA
Statistics
Matches: 172, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
42 170 0.99
43 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTCACTT
Found at i:33801485 original size:28 final size:28
Alignment explanation
Indices: 33801443--33801498 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
33801433 TCCATTCACT
*
33801443 TTTCATTGCACTTAGAGACCCAAGTGTG
1 TTTCATTGCACTTAGAGACCCAACTGTG
* *
33801471 TTTCATTGCATTTAGAGGCCCAACTGTG
1 TTTCATTGCACTTAGAGACCCAACTGTG
33801499 GAGGTCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (28 bp):
TTTCATTGCACTTAGAGACCCAACTGTG
Found at i:33801500 original size:112 final size:112
Alignment explanation
Indices: 33801359--33801561 Score: 352
Period size: 112 Copynumber: 1.8 Consensus size: 112
33801349 TCAATTCACT
** * *
33801359 TTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTGTCATTGCATTTAGAGGTCCAA
1 TTTCATTGCATTTAGAGGCCCAACTGTGGAGGTCAATTTACTTGTCATTGCATTTAGAGGCCCAA
33801424 GTGTGGAGGTCCATTCACTTTTCATTGCACTTAGAGACCCAAGTGTG
66 GTGTGGAGGTCCATTCACTTTTCATTGCACTTAGAGACCCAAGTGTG
* *
33801471 TTTCATTGCATTTAGAGGCCCAACTGTGGAGGTCAATTTACTTTTCATTGCATTTAGAGGCCCAG
1 TTTCATTGCATTTAGAGGCCCAACTGTGGAGGTCAATTTACTTGTCATTGCATTTAGAGGCCCAA
33801536 GTGTGGAGGTCCATTCACTTTTCATT
66 GTGTGGAGGTCCATTCACTTTTCATT
33801562 TCATTTAAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 85 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (112 bp):
TTTCATTGCATTTAGAGGCCCAACTGTGGAGGTCAATTTACTTGTCATTGCATTTAGAGGCCCAA
GTGTGGAGGTCCATTCACTTTTCATTGCACTTAGAGACCCAAGTGTG
Found at i:33801516 original size:70 final size:70
Alignment explanation
Indices: 33801403--33801540 Score: 213
Period size: 70 Copynumber: 2.0 Consensus size: 70
33801393 CATTTACTTG
* * *
33801403 TCATTGCATTTAGAGGTCCAAGTGTGGAGGTCCATTCACTTTTCATTGCACTTAGAGACCCAAGT
1 TCATTGCATTTAGAGGCCCAACTGTGGAGGTCAATTCACTTTTCATTGCACTTAGAGACCCAAGT
33801468 GTGTT
66 GTGTT
* * * *
33801473 TCATTGCATTTAGAGGCCCAACTGTGGAGGTCAATTTACTTTTCATTGCATTTAGAGGCCCAGGT
1 TCATTGCATTTAGAGGCCCAACTGTGGAGGTCAATTCACTTTTCATTGCACTTAGAGACCCAAGT
33801538 GTG
66 GTG
33801541 GAGGTCCATT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (70 bp):
TCATTGCATTTAGAGGCCCAACTGTGGAGGTCAATTCACTTTTCATTGCACTTAGAGACCCAAGT
GTGTT
Found at i:33801530 original size:42 final size:42
Alignment explanation
Indices: 33801471--33801608 Score: 222
Period size: 42 Copynumber: 3.3 Consensus size: 42
33801461 CCCAAGTGTG
** *
33801471 TTTCATTGCATTTAGAGGCCCAACTGTGGAGGTCAATTTACT
1 TTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACT
*
33801513 TTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTCACT
1 TTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACT
* *
33801555 TTTCATTTCATTTAAAGGCCCAGGTGTGGAGGTCCATTTACT
1 TTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACT
33801597 TTTCATTGCATT
1 TTTCATTGCATT
33801609 GTGTATGAAG
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (42 bp):
TTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACT
Found at i:33801601 original size:154 final size:154
Alignment explanation
Indices: 33801321--33801606 Score: 482
Period size: 154 Copynumber: 1.9 Consensus size: 154
33801311 TTCACTTTTG
*
33801321 ATTGCACTTAGAGGCCCAAGTGTGGAGGTCAATTCACTTTTCATTGCATTTAGAGGCCCAGGTGT
1 ATTGCACTTAGAGGCCCAACTGTGGAGGTCAATTCACTTTTCATTGCATTTAGAGGCCCAGGTGT
* * *
33801386 GGAGGTCCATTTACTTGTCATTGCATTTAGAGGTCCAAGTGTGGAGGTCCATTCACTTTTCATTG
66 GGAGGTCCATTCACTTGTCATTGCATTTAAAGGCCCAAGTGTGGAGGTCCATTCACTTTTCATTG
33801451 CACTTAGAGACCCAAGTGTGTTTC
131 CACTTAGAGACCCAAGTGTGTTTC
* *
33801475 ATTGCATTTAGAGGCCCAACTGTGGAGGTCAATTTACTTTTCATTGCATTTAGAGGCCCAGGTGT
1 ATTGCACTTAGAGGCCCAACTGTGGAGGTCAATTCACTTTTCATTGCATTTAGAGGCCCAGGTGT
* * * *
33801540 GGAGGTCCATTCACTTTTCATTTCATTTAAAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTG
66 GGAGGTCCATTCACTTGTCATTGCATTTAAAGGCCCAAGTGTGGAGGTCCATTCACTTTTCATTG
33801605 CA
131 CA
33801607 TTGTGTATGA
Statistics
Matches: 122, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
154 122 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (154 bp):
ATTGCACTTAGAGGCCCAACTGTGGAGGTCAATTCACTTTTCATTGCATTTAGAGGCCCAGGTGT
GGAGGTCCATTCACTTGTCATTGCATTTAAAGGCCCAAGTGTGGAGGTCCATTCACTTTTCATTG
CACTTAGAGACCCAAGTGTGTTTC
Found at i:33802710 original size:153 final size:148
Alignment explanation
Indices: 33802431--33802862 Score: 579
Period size: 153 Copynumber: 2.9 Consensus size: 148
33802421 TTAAAAAAAA
* *
33802431 AGAGAAAGTTTAGATTTTAAAATATAAAAATATGTTTCTTTTAGTCATTTTAAAGGAAAGTTTAA
1 AGAGAAAGTTTAGATTTTAAAAAATAAAAATATGTTTTTTTTAGTCATTTTAAAGGAAAGTTTAA
* *
33802496 ATTTTTAAAACAATATTTTGATTTTTTTTAACTATTTCAAAGTAAAAGCATTAATCTTTAAGAAA
66 ATTTTTAAAACAA-ATTTTGATTTTTTTCAACTATTTCAAAGTAAAAGCTTTAATCTTTAAGAAA
33802561 AATAGTGTGTTTTTTTTTTAAATG
130 AATA--GTG--TTTTTTTTAAA-G
* * * *
33802585 -GAGAAAGTTTAGATTTTAAAAAATAAAAATTTGTTTTTTTTAATCATTTTAAAGAAAATTTTAA
1 AGAGAAAGTTTAGATTTTAAAAAATAAAAATATGTTTTTTTTAGTCATTTTAAAGGAAAGTTTAA
*
33802649 ATTTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAGTAAAAGCTTTAATCTTTAAGGAA
66 ATTTTTAAAACAAA-TTTTGATTTTTTTCAACTATTTCAAAGTAAAAGCTTTAATCTTTAAGAAA
33802714 AATAGTGTTTTTTTTAAAG
130 AATAGTGTTTTTTTTAAAG
* * *
33802733 AGAGAAAGTTTAGATTTTGAAAAA-AAAAATAT-TTTTTTTTAGTCA-TTTAGAGGATAGTTTAA
1 AGAGAAAGTTTAGATTTTAAAAAATAAAAATATGTTTTTTTTAGTCATTTTAAAGGAAAGTTTAA
* * *
33802795 ATTTTTAAAACAAAATTTTGATTTTTTTTTCCAACTATTTCGAAA-T-AAAGTTTTGATTTTTAA
66 ATTTTTAAAAC-AAATTTTGA--TTTTTTT-CAACTATTTC-AAAGTAAAAGCTTTAATCTTTAA
33802858 GAAAA
126 GAAAA
33802863 GTAATAATTT
Statistics
Matches: 251, Mismatches: 20, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
146 30 0.12
147 15 0.06
148 33 0.13
149 44 0.18
150 3 0.01
151 3 0.01
152 1 0.00
153 122 0.49
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (148 bp):
AGAGAAAGTTTAGATTTTAAAAAATAAAAATATGTTTTTTTTAGTCATTTTAAAGGAAAGTTTAA
ATTTTTAAAACAAATTTTGATTTTTTTCAACTATTTCAAAGTAAAAGCTTTAATCTTTAAGAAAA
ATAGTGTTTTTTTTAAAG
Found at i:33802863 original size:19 final size:19
Alignment explanation
Indices: 33802841--33802893 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
33802831 ATTTCGAAAT
*
33802841 AAAGTTTTGATTTTTAAGA
1 AAAGTTTTGATTTTTAAAA
** *
33802860 AAAGTAATAATTTTTTAAAA
1 AAAGTTTTGA-TTTTTAAAA
*
33802880 AAAGCTTTGATTTT
1 AAAGTTTTGATTTT
33802894 ACACCCAAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (19 bp):
AAAGTTTTGATTTTTAAAA
Found at i:33805298 original size:37 final size:37
Alignment explanation
Indices: 33805248--33805320 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
33805238 GGTCTCCTAA
33805248 AGAATGTAGAGGACTGAATAATCGAGTATATCCTTAG
1 AGAATGTAGAGGACTGAATAATCGAGTATATCCTTAG
**
33805285 AGAATGTAGAGGACTGGGTAATCGAGTATATCCTTA
1 AGAATGTAGAGGACTGAATAATCGAGTATATCCTTA
33805321 AGGAAGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (37 bp):
AGAATGTAGAGGACTGAATAATCGAGTATATCCTTAG
Found at i:33806063 original size:41 final size:40
Alignment explanation
Indices: 33805992--33806083 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
33805982 TTTATGGTTT
* *
33805992 TTAGGGTTTAAGGTTAGTGTTTAGTTAAAATAATTTAGGG
1 TTAGGGTTTAAGGGTAGGGTTTAGTTAAAATAATTTAGGG
* * *
33806032 TTAGGGTTATATGGGTAGGGTTTTGTTAAAATAATTTAGGT
1 TTAGGGTT-TAAGGGTAGGGTTTAGTTAAAATAATTTAGGG
*
33806073 TTAAGGTTTAA
1 TTAGGGTTTAA
33806084 AAATTTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 10 0.23
41 34 0.77
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.43
Consensus pattern (40 bp):
TTAGGGTTTAAGGGTAGGGTTTAGTTAAAATAATTTAGGG
Found at i:33806440 original size:126 final size:126
Alignment explanation
Indices: 33806231--33806549 Score: 446
Period size: 126 Copynumber: 2.5 Consensus size: 126
33806221 TTCTTTCAGG
* * * * * *
33806231 AAAATTAATTTTGAGAATACTGTTCTGAA-AAGATAATGTCAGAAACTA-TTCAAGTAGGATGCA
1 AAAAATAATTTTGAGAAGACGGTTCTGAACAA-ATAGTGTCAAAAAC-ACTTCAAGAAGGATGCA
* * *
33806294 CTATCAGTAAAATTACTGAAAAAGGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTTTTGA
64 CTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCTTGA
* *
33806357 AAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACT
1 AAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACACTTCAAGAAGGATGCACT
* * *
33806422 GTCAGCAAATTTGA-TGAAAAAAGCTCCCATGTGGACGCTCTTTTTCTACAGTAGTTCTTGA
66 ATCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCTTGA
* *
33806483 AAAAATAATTTTGAAAAGACGGTTCTGAACAAATAGTGCCAAAAACACTTCAAGAAGGATGCACT
1 AAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACACTTCAAGAAGGATGCACT
33806548 AT
66 AT
33806550 AACACCCCTT
Statistics
Matches: 172, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
126 169 0.98
127 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (126 bp):
AAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACACTTCAAGAAGGATGCACT
ATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCTTGA
Found at i:33808135 original size:37 final size:38
Alignment explanation
Indices: 33808081--33808153 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
33808071 TTTTCATAAT
* *
33808081 TTCACTTTTTCACTTTCAA-TCACTATTCAATTCAAAA
1 TTCACTTTGTCACTTTCAAGTCAATATTCAATTCAAAA
*
33808118 TTCACTTTGTCATTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTGTCACTTTCAAGTCAATATTCAATTCAA
33808154 TTCCACACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 17 0.53
38 15 0.47
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.44
Consensus pattern (38 bp):
TTCACTTTGTCACTTTCAAGTCAATATTCAATTCAAAA
Found at i:33808481 original size:51 final size:51
Alignment explanation
Indices: 33808344--33808740 Score: 342
Period size: 51 Copynumber: 7.8 Consensus size: 51
33808334 ACTTTTATCA
* * *
33808344 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-ATG-TT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
*
33808393 TTACGGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
1 TT-CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * * *
33808445 TTCGGTACACATAGTAGCATTCACTTAGTACTACACATGTGACC--ATCATT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGC-TT
* * * * *
33808495 TATCGATTCACGTAGTAGCCCTCACACAGTACTACACACGTGACTAAAGCTT
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * * * *
33808547 CTCGGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGC-TT
* * * * * * *
33808597 TATTGATTCACGTAATGGCCTTCACACAGTACTACACACATGACCAAAGCTT
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * * * * *
33808649 CTCAGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGC-TT
* * *
33808699 TATCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTG
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTG
33808741 TTCATCGATA
Statistics
Matches: 268, Mismatches: 67, Indels: 24
0.75 0.19 0.07
Matches are distributed among these distances:
49 8 0.03
50 46 0.17
51 202 0.75
52 8 0.03
53 4 0.01
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (51 bp):
TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
Found at i:33808531 original size:102 final size:102
Alignment explanation
Indices: 33808349--33808740 Score: 606
Period size: 102 Copynumber: 3.9 Consensus size: 102
33808339 TATCATTCGA
* * * * ** *
33808349 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCATGTTTTA-CGGTTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
* *
33808413 TTCACATAGTACTACACACGTGACCAAAGCTTTTCGG
66 TTCACACAGTACTACACACGTGACCAAAGCTTCTCGG
*
33808450 TACACATAGTAGCATTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
* *
33808515 CTCACACAGTACTACACACGTGACTAAAGCTTCTCGG
66 TTCACACAGTACTACACACGTGACCAAAGCTTCTCGG
* * * *
33808552 TACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATTGATTCACGTAATGGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
* *
33808617 TTCACACAGTACTACACACATGACCAAAGCTTCTCAG
66 TTCACACAGTACTACACACGTGACCAAAGCTTCTCGG
*
33808654 TACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
33808719 TTCACACAGTACTACACACGTG
66 TTCACACAGTACTACACACGTG
33808741 TTCATCGATA
Statistics
Matches: 265, Mismatches: 25, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
101 40 0.15
102 225 0.85
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (102 bp):
TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
TTCACACAGTACTACACACGTGACCAAAGCTTCTCGG
Found at i:33812977 original size:25 final size:25
Alignment explanation
Indices: 33812949--33812996 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
33812939 ACTTATATTT
*
33812949 TATTAAAA-ATATAAAAATAATTTAC
1 TATTAAAATAT-TAAAAACAATTTAC
33812974 TATTAAAATATTAAAAACAATTT
1 TATTAAAATATTAAAAACAATTT
33812997 TTATTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
TATTAAAATATTAAAAACAATTTAC
Found at i:33813001 original size:24 final size:24
Alignment explanation
Indices: 33812946--33813001 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
33812936 AGAACTTATA
*
33812946 TTTTATTAAAAATATAAAAATAAT
1 TTTTATTAAAAATATAAAAACAAT
*
33812970 TTACTATT-AAAATATTAAAAACAAT
1 TT-TTATTAAAAATA-TAAAAACAAT
33812995 TTTTATT
1 TTTTATT
33813002 TTATTAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTTATTAAAAATATAAAAACAAT
Found at i:33813424 original size:18 final size:18
Alignment explanation
Indices: 33813403--33813437 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33813393 GAAAAGGAAA
*
33813403 CATATAAGGGTTAGGATC
1 CATATAAGGGCTAGGATC
33813421 CATATAAGGGCTAGGAT
1 CATATAAGGGCTAGGAT
33813438 ACGCATCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (18 bp):
CATATAAGGGCTAGGATC
Found at i:33815257 original size:30 final size:30
Alignment explanation
Indices: 33815192--33815260 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
33815182 ATTAATTAAA
*
33815192 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
1 GAGAGTTTTGAGAAATTTAAGGAGAAATTT
* * *
33815222 GAGAGTTTTGATAAATTTAGGGAGAATTTT
1 GAGAGTTTTGAGAAATTTAAGGAGAAATTT
33815252 GAGAGTTTT
1 GAGAGTTTT
33815261 TTGCCAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.35, C:0.01, G:0.28, T:0.36
Consensus pattern (30 bp):
GAGAGTTTTGAGAAATTTAAGGAGAAATTT
Found at i:33815748 original size:41 final size:41
Alignment explanation
Indices: 33815702--33815783 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
33815692 AAAAAGTTAA
*
33815702 ATTATTTCTTTTAATTGACATATTAATTAAAACGTTAATAT
1 ATTATTTCTTTTAATTGAAATATTAATTAAAACGTTAATAT
33815743 ATTATTTCTTTTAATTGAAATATTAATTAAAACGTTAATAT
1 ATTATTTCTTTTAATTGAAATATTAATTAAAACGTTAATAT
33815784 TTTTAACGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (41 bp):
ATTATTTCTTTTAATTGAAATATTAATTAAAACGTTAATAT
Found at i:33816034 original size:16 final size:16
Alignment explanation
Indices: 33815998--33816052 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
33815988 CACTTGTATA
*
33815998 ATTTTTATTTGTTA-TT
1 ATTTTTATCT-TTATTT
33816014 A-TTTTATCTTTATTT
1 ATTTTTATCTTTATTT
* *
33816029 ATTTTTATGTTCATTT
1 ATTTTTATCTTTATTT
*
33816045 ATATTTAT
1 ATTTTTAT
33816053 GTTTTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 3 0.09
15 10 0.30
16 20 0.61
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.71
Consensus pattern (16 bp):
ATTTTTATCTTTATTT
Found at i:33816053 original size:16 final size:15
Alignment explanation
Indices: 33816012--33816055 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
33816002 TTATTTGTTA
* *
33816012 TTATTTTATCTTTAT
1 TTATTTTATGTTCAT
33816027 TTATTTTTATGTTCAT
1 TTA-TTTTATGTTCAT
33816043 TTATATTTATGTT
1 TTAT-TTTATGTT
33816056 TTTTTTACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (15 bp):
TTATTTTATGTTCAT
Found at i:33822018 original size:146 final size:145
Alignment explanation
Indices: 33821846--33822119 Score: 381
Period size: 146 Copynumber: 1.9 Consensus size: 145
33821836 TTTTATGATG
* * *
33821846 AAAAATTTAAGATTTACTACAAATTGTTAAA-TTTCAATT-AGATATTGAATTTTACTCAATTCT
1 AAAAATTTAAGATTTACTACAAATTGTCAAATTTTCAATTGA-AGATTGAATTTTACCCAATTCT
* * **
33821909 TTATTTTTTTTCCATACTTAAAATAATTATATTATATTAGTAACACTTTCTATAATTTGCCCATT
65 GTATTTCTTTT-CATACCCAAAATAATTATATTATATTAGTAACACTTTCTATAATTTGCCCATT
33821974 TTATTAATTTACAACTA
129 TTATTAATTTACAACTA
* * * *
33821991 AAAAATATTAAGATTTATTACATATTGTCAAATTTTCAGTTGAAGATTGATTTTTACCCAATTCT
1 AAAAAT-TTAAGATTTACTACAAATTGTCAAATTTTCAATTGAAGATTGAATTTTACCCAATTCT
* * *
33822056 GTATTTCTTTTCATACCCAAAATAATTATATTATATTAGTAACACTTTTTGTAGTTTGCCCATT
65 GTATTTCTTTTCATACCCAAAATAATTATATTATATTAGTAACACTTTCTATAATTTGCCCATT
33822120 CTTTGCGTAC
Statistics
Matches: 112, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
145 6 0.05
146 70 0.62
147 35 0.31
148 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.46
Consensus pattern (145 bp):
AAAAATTTAAGATTTACTACAAATTGTCAAATTTTCAATTGAAGATTGAATTTTACCCAATTCTG
TATTTCTTTTCATACCCAAAATAATTATATTATATTAGTAACACTTTCTATAATTTGCCCATTTT
ATTAATTTACAACTA
Found at i:33827147 original size:3 final size:3
Alignment explanation
Indices: 33827139--33827186 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
33827129 TTAAATTAAG
* * *
33827139 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT ATT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33827187 TAATTAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:33827190 original size:4 final size:4
Alignment explanation
Indices: 33827181--33827209 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
33827171 TATTAATAAT
33827181 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
33827210 AGAAAACGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:33827605 original size:5 final size:5
Alignment explanation
Indices: 33827593--33827622 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
33827583 ATTAAATTGA
*
33827593 AGTGG AGTAG AGTGG AGTGG AGTGG AGTGG
1 AGTGG AGTGG AGTGG AGTGG AGTGG AGTGG
33827623 TGCGGGGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.57, T:0.20
Consensus pattern (5 bp):
AGTGG
Found at i:33828729 original size:2 final size:2
Alignment explanation
Indices: 33828722--33828767 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
33828712 TTTTACCAAT
33828722 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33828764 TA TA
1 TA TA
33828768 CACGTATGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33829090 original size:4 final size:4
Alignment explanation
Indices: 33829081--33829135 Score: 101
Period size: 4 Copynumber: 13.8 Consensus size: 4
33829071 AGTAGTTATA
*
33829081 TATG TATG TATG TATG CATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
33829129 TATG TAT
1 TATG TAT
33829136 TAATAATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.25, C:0.02, G:0.24, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:33831840 original size:18 final size:17
Alignment explanation
Indices: 33831798--33831841 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
33831788 TGTTGTTCGT
33831798 TTTCAAAACATTATTCA
1 TTTCAAAACATTATTCA
* *
33831815 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTC-A
33831834 TTTCAAAA
1 TTTCAAAA
33831842 TGTTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (17 bp):
TTTCAAAACATTATTCA
Found at i:33833880 original size:13 final size:14
Alignment explanation
Indices: 33833856--33833886 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
33833846 AGGAAACCGT
33833856 GAAAAATCGAAGAA
1 GAAAAATCGAAGAA
33833870 GAAAAAT-GAAGAA
1 GAAAAATCGAAGAA
33833883 GAAA
1 GAAA
33833887 GTCGACGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.68, C:0.03, G:0.23, T:0.06
Consensus pattern (14 bp):
GAAAAATCGAAGAA
Found at i:33835147 original size:21 final size:24
Alignment explanation
Indices: 33835098--33835144 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
33835088 ATCATTAATG
*
33835098 ATTTATAAAAATGAATAACAAAATA
1 ATTTAAAAAAAT-AATAACAAAATA
33835123 ATTTAAAAAAAT-ATAA-AAAATA
1 ATTTAAAAAAATAATAACAAAATA
33835145 TTTTGTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 4 0.19
25 11 0.52
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (24 bp):
ATTTAAAAAAATAATAACAAAATA
Found at i:33835798 original size:21 final size:21
Alignment explanation
Indices: 33835755--33835799 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
33835745 GTATTCTTTG
*
33835755 TATTATTATTAATAATAATAT
1 TATTATTATTAATAATAACAT
*
33835776 TATTATTATTTCATAAT-ACAT
1 TATTATTA-TTAATAATAACAT
33835797 TAT
1 TAT
33835800 CAACACGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTATTATTAATAATAACAT
Found at i:33843054 original size:289 final size:289
Alignment explanation
Indices: 33842587--33843167 Score: 955
Period size: 289 Copynumber: 2.0 Consensus size: 289
33842577 TTCTTTCTCT
** *
33842587 AGTACAAGTCCCACCCACTGAATTTTATAGATAGGATCCATGATCCTTGCTTTAAACCATTAAGA
1 AGTACAAGTCCCACCCACTGAACGTCATAGATAGGATCCATGATCCTTGCTTTAAACCATTAAGA
* *
33842652 CTCGAGTTTCCCAAGATCAAATACTCGAGATTGAATCAAATTGTTTTGTCCCTTGACAGATCTCT
66 CTCGAGTTTCCCAAGATCAAATACTCGAGATTGAATCAAACTGTTTTGTCCCTTGACAGATCCCT
33842717 TTTCAGTATTTGAAATAGTCCACTCGATACCTTTCTCGTGCCTTTTCAAAATAGTGAAGTCTAAC
131 TTTCAGTATTTGAAATAGTCCACTCGATACCTTTCTCGTGCCTTTTCAAAATAGTGAAGTCTAAC
* * *
33842782 TCGGATGGCTCTTCTCTTGATGGGTTGGGTTGCTTGTACTCATGTGATGATAGCTCTAATGACTC
196 TCGGATGACTCTTCTCTTGATGGGTTGGGTTCCTTGTACTAATGTGATGATAGCTCTAATGACTC
* *
33842847 GAATTTAACTTTTGAACTAAATTCTTCCA
261 AAATTTAAATTTTGAACTAAATTCTTCCA
* * * *
33842876 AGTACAAGTCCCACCCACTGAACGTCATAGATGGGATCCATTATCCTTGCTTTTAACCATTGAGA
1 AGTACAAGTCCCACCCACTGAACGTCATAGATAGGATCCATGATCCTTGCTTTAAACCATTAAGA
* * * * *
33842941 CTTGAGTTTTCCAGGATCAAATACTCGAGATTGAATCGAACTGTTTTGTCCCTTTACAGATCCCT
66 CTCGAGTTTCCCAAGATCAAATACTCGAGATTGAATCAAACTGTTTTGTCCCTTGACAGATCCCT
* * *
33843006 TTTCAGTATTTGTAATAGTCCACTCGATACCTTTCTCGTTCTTTTTCAAAATAGTGAAGTCTAAC
131 TTTCAGTATTTGAAATAGTCCACTCGATACCTTTCTCGTGCCTTTTCAAAATAGTGAAGTCTAAC
*
33843071 TCGGATGACTCTTCTCTTGATGGGTTGGTTTCCTTGTACTAATGTGATGATAGCTCTAATGACTC
196 TCGGATGACTCTTCTCTTGATGGGTTGGGTTCCTTGTACTAATGTGATGATAGCTCTAATGACTC
33843136 AAATTTAAATTTTGAACTAAATTCTTCCA
261 AAATTTAAATTTTGAACTAAATTCTTCCA
33843165 AGT
1 AGT
33843168 TAGCTTCCAA
Statistics
Matches: 269, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
289 269 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (289 bp):
AGTACAAGTCCCACCCACTGAACGTCATAGATAGGATCCATGATCCTTGCTTTAAACCATTAAGA
CTCGAGTTTCCCAAGATCAAATACTCGAGATTGAATCAAACTGTTTTGTCCCTTGACAGATCCCT
TTTCAGTATTTGAAATAGTCCACTCGATACCTTTCTCGTGCCTTTTCAAAATAGTGAAGTCTAAC
TCGGATGACTCTTCTCTTGATGGGTTGGGTTCCTTGTACTAATGTGATGATAGCTCTAATGACTC
AAATTTAAATTTTGAACTAAATTCTTCCA
Found at i:33845667 original size:21 final size:18
Alignment explanation
Indices: 33845622--33845667 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 18
33845612 AAAAATAACA
33845622 AAAAAATAAATAATAAAG
1 AAAAAATAAATAATAAAG
33845640 AATAAAATAGGAATAATAAAGG
1 AA-AAAATA--AATAATAAA-G
33845662 AAAAAA
1 AAAAAA
33845668 GTTAAAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 6 0.25
21 13 0.54
22 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (18 bp):
AAAAAATAAATAATAAAG
Found at i:33845710 original size:11 final size:11
Alignment explanation
Indices: 33845694--33845718 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33845684 GTAAATTTAT
33845694 AAATAAAATAA
1 AAATAAAATAA
33845705 AAATAAAATAA
1 AAATAAAATAA
33845716 AAA
1 AAA
33845719 CCAAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:33850794 original size:14 final size:14
Alignment explanation
Indices: 33850775--33850803 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
33850765 ATCTATGGAC
33850775 TTACCTCGCCACCA
1 TTACCTCGCCACCA
33850789 TTACCTCGCCACCA
1 TTACCTCGCCACCA
33850803 T
1 T
33850804 AAAAGTGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.48, G:0.07, T:0.24
Consensus pattern (14 bp):
TTACCTCGCCACCA
Found at i:33852118 original size:19 final size:20
Alignment explanation
Indices: 33852091--33852135 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
33852081 CTTGGTAAAT
*
33852091 ACATGTGTA-ATAATAATAA
1 ACATATGTATATAATAATAA
*
33852110 ACATATGTATTTAATAATAA
1 ACATATGTATATAATAATAA
33852130 A-ATATG
1 ACATATG
33852136 AATTTCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (20 bp):
ACATATGTATATAATAATAA
Found at i:33852140 original size:19 final size:20
Alignment explanation
Indices: 33852101--33852140 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
33852091 ACATGTGTAA
*
33852101 TAATAATAAACATATGTATT
1 TAATAATAAACATATGAATT
33852121 TAATAATAAA-ATATGAATT
1 TAATAATAAACATATGAATT
33852140 T
1 T
33852141 CTTATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (20 bp):
TAATAATAAACATATGAATT
Found at i:33853280 original size:40 final size:40
Alignment explanation
Indices: 33853162--33853292 Score: 135
Period size: 40 Copynumber: 3.3 Consensus size: 40
33853152 TTTGAGTCGG
* * *
33853162 TGAGACAGTGGGTGTCAATTTATTACTTCGAATTAATTTC-A
1 TGAGACACTGGGTGTCAAATTATTACTTCGAATT-A-TCCGA
* * ** *
33853203 TGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTAGCCGA
1 TGAGACACTGGGTGTCAAATTATTACTTCGAATTATCCGA
33853240 TGAGACACTGGGTGTCAAATTATTACTTCGAATTATCCGA
1 TGAGACACTGGGTGTCAAATTATTACTTCGAATTATCCGA
*
33853280 TGAGGCACTGGGT
1 TGAGACACTGGGT
33853293 ACCAAACTGG
Statistics
Matches: 72, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
36 1 0.01
37 15 0.21
38 13 0.18
39 2 0.03
40 29 0.40
41 12 0.17
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TGAGACACTGGGTGTCAAATTATTACTTCGAATTATCCGA
Found at i:33858772 original size:25 final size:24
Alignment explanation
Indices: 33858722--33858766 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
33858712 TTACCATTCT
*
33858722 TTTTTATTATTTTATTTTATTTTA
1 TTTTTATTACTTTATTTTATTTTA
*
33858746 TTTTTATTACTTT-CTTTATTT
1 TTTTTATTACTTTATTTTATTT
33858767 GTTATTCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTTATTACTTTATTTTATTTTA
Found at i:33860215 original size:6 final size:6
Alignment explanation
Indices: 33860206--33860247 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
33860196 TTTGTTTTCT
* *
33860206 TTTTAA TTTTAA TTTTAA TTTTAA TTTTTA TGTTTAT TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T-TTTAA TTTTA
33860248 TCTTTAGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
6 28 0.88
7 4 0.12
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:33860241 original size:25 final size:24
Alignment explanation
Indices: 33860217--33860277 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
33860207 TTTAATTTTA
*
33860217 ATTTTAATTTTAATTTTTATGTTT
1 ATTTTTATTTTAATTTTTATGTTT
*
33860241 ATTTTTATCTTTAGTTGTTT-TGTTT
1 ATTTTTAT-TTTAATT-TTTATGTTT
33860266 CATTTTTATTTT
1 -ATTTTTATTTT
33860278 CTTGTACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 7 0.22
25 14 0.44
26 11 0.34
ACGTcount: A:0.18, C:0.03, G:0.07, T:0.72
Consensus pattern (24 bp):
ATTTTTATTTTAATTTTTATGTTT
Found at i:33860248 original size:6 final size:6
Alignment explanation
Indices: 33860200--33860277 Score: 50
Period size: 6 Copynumber: 12.5 Consensus size: 6
33860190 ATTTTATTTG
* * * * *
33860200 TTTTCT TTTTAAT TTTAAT TTTAAT TTTAAT TTTTAT GTTTAT TTTTAT
1 TTTTAT TTTT-AT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* *
33860249 CTTTAGT TGTTT-T GTTTCAT TTTTAT TTT
1 TTTTA-T T-TTTAT -TTTTAT TTTTAT TTT
33860278 CTTGTACTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
6 48 0.83
7 7 0.12
8 3 0.05
ACGTcount: A:0.18, C:0.04, G:0.05, T:0.73
Consensus pattern (6 bp):
TTTTAT
Found at i:33870356 original size:2 final size:2
Alignment explanation
Indices: 33870349--33870376 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33870339 TTTTACAATT
33870349 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
33870377 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:33873199 original size:15 final size:16
Alignment explanation
Indices: 33873168--33873203 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
33873158 CATGGCTTTG
33873168 TTTATTTTTGTTAATT
1 TTTATTTTTGTTAATT
*
33873184 TTTATTTTT-TTCATT
1 TTTATTTTTGTTAATT
33873199 TTTAT
1 TTTAT
33873204 AAATAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTATTTTTGTTAATT
Found at i:33879882 original size:42 final size:44
Alignment explanation
Indices: 33879835--33879933 Score: 107
Period size: 45 Copynumber: 2.3 Consensus size: 44
33879825 GCACATAAGT
33879835 GCTAAACGGAAACCCGTA-AAG-GTTAAAC-G-AAAGCTCAAAAGA
1 GCTAAACGGAAA-CC-TAGAAGAGTTAAACTGCAAAGCTCAAAAGA
* * **
33879877 GCTAAACTGAAACCTAGAAGAGTTAAACTGCTGAAGCTCATGAGA
1 GCTAAACGGAAACCTAGAAGAGTTAAACTGC-AAAGCTCAAAAGA
33879922 GCTAAACGGAAA
1 GCTAAACGGAAA
33879934 GCAAACATGG
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
40 2 0.04
41 5 0.11
42 18 0.38
43 1 0.02
45 21 0.45
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.15
Consensus pattern (44 bp):
GCTAAACGGAAACCTAGAAGAGTTAAACTGCAAAGCTCAAAAGA
Found at i:33882504 original size:14 final size:15
Alignment explanation
Indices: 33882482--33882525 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
33882472 ATTTCAATAC
33882482 TTTTAATAATA-TAT
1 TTTTAATAATATTAT
*
33882496 TTTTGATAATATTAT
1 TTTTAATAATATTAT
*
33882511 TTTAAATTAATATTA
1 TTTTAA-TAATATTA
33882526 ATACTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 10 0.40
15 7 0.28
16 8 0.32
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TTTTAATAATATTAT
Found at i:33882561 original size:21 final size:21
Alignment explanation
Indices: 33882517--33882561 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
33882507 TTATTTTAAA
* *
33882517 TTAATATTAATACTTTTTTGT
1 TTAATATTAATACTTTTATAT
33882538 TTAATATT-ATGACTTTTATAT
1 TTAATATTAAT-ACTTTTATAT
33882559 TTA
1 TTA
33882562 TTCATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (21 bp):
TTAATATTAATACTTTTATAT
Found at i:33885769 original size:14 final size:14
Alignment explanation
Indices: 33885750--33885779 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
33885740 AAGTAGCCAA
33885750 CCTTTGCCTTATAG
1 CCTTTGCCTTATAG
33885764 CCTTTGCCTTATAG
1 CCTTTGCCTTATAG
33885778 CC
1 CC
33885780 ATTGACGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.33, G:0.13, T:0.40
Consensus pattern (14 bp):
CCTTTGCCTTATAG
Found at i:33889339 original size:137 final size:137
Alignment explanation
Indices: 33889093--33889366 Score: 530
Period size: 137 Copynumber: 2.0 Consensus size: 137
33889083 GTTGGTGAAA
*
33889093 GCAAAGGCAAGAATTAAACAATGGACACAAATAATTTAGAGTGGTTCGACCCCAATTGCCTACTT
1 GCAAAGGCAAGAATTAAACAATGAACACAAATAATTTAGAGTGGTTCGACCCCAATTGCCTACTT
*
33889158 CACTACCTTAGCTTTCCACCACTAAGGATTTTTCCAATTTCACTAATTTTTTCACCCTTTGAGGA
66 CACTACCTTAGCTTTCCACCACTAAGGATTTTTCCAATTTCACTAATTTTTTCAACCTTTGAGGA
33889223 CAAGGTT
131 CAAGGTT
33889230 GCAAAGGCAAGAATTAAACAATGAACACAAATAATTTAGAGTGGTTCGACCCCAATTGCCTACTT
1 GCAAAGGCAAGAATTAAACAATGAACACAAATAATTTAGAGTGGTTCGACCCCAATTGCCTACTT
33889295 CACTACCTTAGCTTTCCACCACTAAGGATTTTTCCAATTTCACTAATTTTTTCAACCTTTGAGGA
66 CACTACCTTAGCTTTCCACCACTAAGGATTTTTCCAATTTCACTAATTTTTTCAACCTTTGAGGA
33889360 CAAGGTT
131 CAAGGTT
33889367 TAACCTTACA
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 135 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (137 bp):
GCAAAGGCAAGAATTAAACAATGAACACAAATAATTTAGAGTGGTTCGACCCCAATTGCCTACTT
CACTACCTTAGCTTTCCACCACTAAGGATTTTTCCAATTTCACTAATTTTTTCAACCTTTGAGGA
CAAGGTT
Found at i:33890101 original size:20 final size:20
Alignment explanation
Indices: 33890058--33890106 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
33890048 AATCATTTTG
* * *
33890058 AAATGATTTTGACTTGATTG
1 AAATCATTTTGACATGATTA
*
33890078 AAATCATTTTGACATGGTTA
1 AAATCATTTTGACATGATTA
33890098 AAATCATTT
1 AAATCATTT
33890107 ACACTTGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (20 bp):
AAATCATTTTGACATGATTA
Found at i:33891814 original size:21 final size:23
Alignment explanation
Indices: 33891764--33891817 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
33891754 TAGATCACAA
*
33891764 GGCTATGT-CCTTAGGTCACACG
1 GGCTATGTGCCTTAGGCCACACG
*
33891786 GGCT-TGTGCCTTA-GCCATAC-
1 GGCTATGTGCCTTAGGCCACACG
33891806 GGCTATGTGCCT
1 GGCTATGTGCCT
33891818 ACTTCCAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 4 0.14
21 15 0.54
22 9 0.32
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.30
Consensus pattern (23 bp):
GGCTATGTGCCTTAGGCCACACG
Found at i:33893486 original size:20 final size:21
Alignment explanation
Indices: 33893461--33893512 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
33893451 CACTAATAAG
* *
33893461 AAGATAGAAAAA-AATAAAAT
1 AAGATAGAAAAATAACAAAAC
33893481 AAGATA-AAAATATAACAAAAC
1 AAGATAGAAAA-ATAACAAAAC
33893502 AAG-TAGAAAAA
1 AAGATAGAAAAA
33893513 CAATTGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 4 0.15
20 10 0.37
21 13 0.48
ACGTcount: A:0.73, C:0.04, G:0.10, T:0.13
Consensus pattern (21 bp):
AAGATAGAAAAATAACAAAAC
Found at i:33898341 original size:20 final size:20
Alignment explanation
Indices: 33898318--33898360 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
33898308 CAAATTTATT
* *
33898318 GATACTTTTATAAAGATATC
1 GATACTTGTATAAAAATATC
33898338 GATACTTGTATAAAAATATC
1 GATACTTGTATAAAAATATC
33898358 GAT
1 GAT
33898361 GCCTATTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (20 bp):
GATACTTGTATAAAAATATC
Found at i:33900288 original size:17 final size:19
Alignment explanation
Indices: 33900253--33900289 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
33900243 GTAAAAATGA
33900253 ATGTCAAATTTTTTAATTT
1 ATGTCAAATTTTTTAATTT
33900272 ATGTC-AATTTTTT-ATTT
1 ATGTCAAATTTTTTAATTT
33900289 A
1 A
33900290 GGCCTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 8 0.44
19 5 0.28
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
ATGTCAAATTTTTTAATTT
Found at i:33905150 original size:21 final size:21
Alignment explanation
Indices: 33905108--33905153 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
33905098 ACTTGAACTA
*
33905108 AATAATCAAATTCAATCCATTC
1 AATAATC-AATTCAATCAATTC
33905130 AATAATC-ATTCTAATCAATTC
1 AATAATCAATTC-AATCAATTC
33905151 AAT
1 AAT
33905154 CCATAAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 11 0.50
22 7 0.32
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAATCAATTCAATCAATTC
Found at i:33912100 original size:20 final size:20
Alignment explanation
Indices: 33912075--33912160 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 20
33912065 TTGTATGGGA
33912075 TTGCACTTTGGTGCCTCTAT
1 TTGCACTTTGGTGCCTCTAT
*
33912095 TTGCACTTCGGTGCCTCT-T
1 TTGCACTTTGGTGCCTCTAT
* * *
33912114 CTTACACTTTGGTGTCTCTGT
1 -TTGCACTTTGGTGCCTCTAT
* * * *
33912135 TTGCACTATGATGACTCTAA
1 TTGCACTTTGGTGCCTCTAT
33912155 TTGCAC
1 TTGCAC
33912161 AATTGTTCCT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
19 1 0.02
20 52 0.96
21 1 0.02
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.42
Consensus pattern (20 bp):
TTGCACTTTGGTGCCTCTAT
Found at i:33914540 original size:27 final size:26
Alignment explanation
Indices: 33914510--33914566 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 26
33914500 ATCCTAATTC
33914510 TAAAAAAATTCAAATACATATAATACA
1 TAAAAAAATTCAAATACATATAATA-A
* ** * *
33914537 TAAATATTTTTAAATATATATAATAA
1 TAAAAAAATTCAAATACATATAATAA
33914563 TAAA
1 TAAA
33914567 TTTAAAACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAAAAAATTCAAATACATATAATAA
Found at i:33915237 original size:9 final size:9
Alignment explanation
Indices: 33915223--33915271 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
33915213 TATTTTTATA
33915223 TTAAAATAT
1 TTAAAATAT
33915232 TTAAAATAAT
1 TTAAAAT-AT
* *
33915242 TTATATTAT
1 TTAAAATAT
*
33915251 ATTAAAATGT
1 -TTAAAATAT
33915261 TTAAAATAT
1 TTAAAATAT
33915270 TT
1 TT
33915272 TATTTTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 19 0.59
10 13 0.41
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (9 bp):
TTAAAATAT
Found at i:33915252 original size:29 final size:29
Alignment explanation
Indices: 33915218--33915274 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
33915208 TTTTTTATTT
33915218 TTATATTAAAATATTTAAAATAATTTATA
1 TTATATTAAAATATTTAAAATAATTTATA
* *
33915247 TTATATTAAAATGTTTAAAATATTTTAT
1 TTATATTAAAATATTTAAAATAATTTAT
33915275 TTTTATACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
TTATATTAAAATATTTAAAATAATTTATA
Found at i:33915761 original size:67 final size:67
Alignment explanation
Indices: 33915681--33915809 Score: 195
Period size: 67 Copynumber: 1.9 Consensus size: 67
33915671 AATATATCAT
33915681 CCTACAATCACATACAAAAAGTTATATTACTCCACCACCACACCCATTTACACATACAAAAAATG
1 CCTACAATCACATACAAAAAGTTATATTACTCCACCACCACACCCATTTACACATACAAAAAATG
33915746 AA
66 AA
* * * * * * *
33915748 CCTACAATTACATACAAAAAGTTATATTAGTTCACCACCACATCTATTTACGCATACCAAAA
1 CCTACAATCACATACAAAAAGTTATATTACTCCACCACCACACCCATTTACACATACAAAAA
33915810 GTGACAACCC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 55 1.00
ACGTcount: A:0.44, C:0.28, G:0.04, T:0.24
Consensus pattern (67 bp):
CCTACAATCACATACAAAAAGTTATATTACTCCACCACCACACCCATTTACACATACAAAAAATG
AA
Found at i:33918878 original size:31 final size:31
Alignment explanation
Indices: 33918840--33918902 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
33918830 GATTCGGATG
33918840 ATGTTCTCATTTGTTTATCTTGAAAATAGAA
1 ATGTTCTCATTTGTTTATCTTGAAAATAGAA
33918871 ATGTTCTCATTTGTTTATCTTGAAAATAGAA
1 ATGTTCTCATTTGTTTATCTTGAAAATAGAA
33918902 A
1 A
33918903 ATAGACTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (31 bp):
ATGTTCTCATTTGTTTATCTTGAAAATAGAA
Found at i:33920209 original size:23 final size:23
Alignment explanation
Indices: 33920178--33920228 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
33920168 ACCTATTTTC
* * *
33920178 TTACTGTAGTAATTTTTGGGGTA
1 TTACAGTAGTAATTTTTAGGATA
33920201 TTACAGTAGTAATTTTTAGGATA
1 TTACAGTAGTAATTTTTAGGATA
33920224 TTACA
1 TTACA
33920229 ACGAATCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (23 bp):
TTACAGTAGTAATTTTTAGGATA
Found at i:33927752 original size:2 final size:2
Alignment explanation
Indices: 33927745--33927784 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
33927735 TATCTGTTTT
33927745 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33927785 AAGCCTAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33936562 original size:3 final size:3
Alignment explanation
Indices: 33936554--33936605 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
33936544 ATAAATTGGT
* * * *
33936554 TTA TTA TTA TTA TTA TTA TTA TTA CTTG TCA CTA TTAA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT-A TTA TTA TTA
33936601 TTA TT
1 TTA TT
33936606 CATCAATTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
3 34 0.87
4 5 0.13
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:33937006 original size:18 final size:20
Alignment explanation
Indices: 33936980--33937019 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
33936970 CCCCTTTTAC
33936980 ATATATTA-TTATA-TAAAT
1 ATATATTATTTATATTAAAT
*
33936998 ATATCTTATTTATATTAAAT
1 ATATATTATTTATATTAAAT
33937018 AT
1 AT
33937020 TTCATTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATTATTTATATTAAAT
Found at i:33939702 original size:23 final size:23
Alignment explanation
Indices: 33939682--33939726 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
33939672 TAGCACTTTG
* *
33939682 GTGCGATTCATTTTGGCACTTCA
1 GTGCGATCCATTCTGGCACTTCA
*
33939705 GTGGGATCCATTCTGGCACTTC
1 GTGCGATCCATTCTGGCACTTC
33939727 TTTGCAACTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (23 bp):
GTGCGATCCATTCTGGCACTTCA
Found at i:33941294 original size:24 final size:23
Alignment explanation
Indices: 33941262--33941316 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
33941252 ACCACTAATA
33941262 AAAATATGCAAAAAATCCTGCCAGT
1 AAAA-ATGCAAAAAA-CCTGCCAGT
* * *
33941287 AAAAATGCAGACAAGCTGCCAGT
1 AAAAATGCAAAAAACCTGCCAGT
33941310 AAAAATG
1 AAAAATG
33941317 TGATAAATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 15 0.56
24 8 0.30
25 4 0.15
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.16
Consensus pattern (23 bp):
AAAAATGCAAAAAACCTGCCAGT
Found at i:33947883 original size:34 final size:34
Alignment explanation
Indices: 33947840--33947908 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
33947830 AGGACAGGAA
33947840 TGTTTAACGTGAAAATTGTAGGTGGAGGGTGGCT
1 TGTTTAACGTGAAAATTGTAGGTGGAGGGTGGCT
33947874 TGTTTAACGTGAAAATTGTAGGTGGAGGGTGGCT
1 TGTTTAACGTGAAAATTGTAGGTGGAGGGTGGCT
33947908 T
1 T
33947909 TTAGGTTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.23, C:0.06, G:0.38, T:0.33
Consensus pattern (34 bp):
TGTTTAACGTGAAAATTGTAGGTGGAGGGTGGCT
Found at i:33950343 original size:28 final size:27
Alignment explanation
Indices: 33950294--33950350 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 27
33950284 AAAACGGTAA
33950294 TTTTACCCTTAGGGGTATTTTGGTCAT
1 TTTTACCCTTAGGGGTATTTTGGTCAT
* *
33950321 TTTTACCCTTCGAGGGTATTTTGTTCAT
1 TTTTACCCTTAG-GGGTATTTTGGTCAT
33950349 TT
1 TT
33950351 AACAACCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (27 bp):
TTTTACCCTTAGGGGTATTTTGGTCAT
Found at i:33953738 original size:49 final size:49
Alignment explanation
Indices: 33953675--33953907 Score: 184
Period size: 49 Copynumber: 4.8 Consensus size: 49
33953665 ATAAGATGGG
* * * *
33953675 CCACTAGTAGGGCATATTAGTTGCTAACCAGATTGGTAGATGTGAAAGA
1 CCACTGGTAGGGCATGTTAGTTGCTAACTAGATTGGTAGATATGAAAGA
* * * * *
33953724 CCACTGGTAAGGCATGTTAGTTGCTAACCAGATGGGT-GA-ATAAAATGGG
1 CCACTGGTAGGGCATGTTAGTTGCTAACTAGATTGGTAGATATGAAA--GA
* ** *
33953773 TCACTGGTAGGGCATGTTAGGTT-CTAACTAGATTGACAGATGTGAAAGA
1 CCACTGGTAGGGCATGTTA-GTTGCTAACTAGATTGGTAGATATGAAAGA
** * * * * * * * **
33953822 TGACTAGTAAGACTTGTTAGTTGCTAACTAGATGGGTAAATAAGGTAGA
1 CCACTGGTAGGGCATGTTAGTTGCTAACTAGATTGGTAGATATGAAAGA
* *
33953871 CCATTGGTAGGGTATGTTAGTTGCTAACTAGATTGGT
1 CCACTGGTAGGGCATGTTAGTTGCTAACTAGATTGGT
33953908 GTGAGCGCTG
Statistics
Matches: 140, Mismatches: 38, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
47 4 0.03
48 5 0.04
49 122 0.87
50 5 0.04
51 4 0.03
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.29
Consensus pattern (49 bp):
CCACTGGTAGGGCATGTTAGTTGCTAACTAGATTGGTAGATATGAAAGA
Done.